IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On the Approximability of Some Haplotyping Problems
AAIM '09 Proceedings of the 5th International Conference on Algorithmic Aspects in Information and Management
The longest haplotype reconstruction problem revisited
FCT'09 Proceedings of the 17th international conference on Fundamentals of computation theory
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
New results for the Longest Haplotype Reconstruction problem
Discrete Applied Mathematics
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
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We present several new results pertaining to haplotyping. These results concern the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype fragments. We consider the complexity of the problems Minimum Error Correction (MEC) and Longest Haplotype Reconstruction (LHR) for different restrictions on the input data. Specifically, we look at the gapless case, where every row of the input corresponds to a gapless haplotype-fragment, and the 1-gap case, where at most one gap per fragment is allowed. We prove that MEC is APX-hard in the 1-gap case and still NP-hard in the gapless case. In addition, we question earlier claims that MEC is NP-hard even when the input matrix is restricted to being completely binary. Concerning LHR, we show that this problem is NP-hard and APX-hard in the 1-gap case (and thus also in the general case), but is polynomial time solvable in the gapless case.